I can't see the link between playing through the app (that is linked to me to the fact that my PC stays at home but not me) and the progresses I made in the game...
Some people can also go on holidays or have their Internet down for a long time (my case), even when they reached the last chapter...
I also don't think usefull to hide the quests you can't complete through the app because something isn't yet developed for it : If you see a quest you can't complete through the app, you know it's time to swap to (or find a) PC for a while (if you have one) and won't destroy your settlement thinking you ended the storyline for this chapter (what I thought and that I was close to do !!!)
...my opinion.
But thanks for replying anyway, I'm glad to know this was intended this way (even if it's another bad idea imo) and not a bug or the need to buy a new smartphone to sustain the growing of the app version...
"not-a-bug" unsolved but explained